Table 1 Sequenced cultivars and proportions derived from the ancestral species C. reticulata and C. maxima

Cultivar	Abbreviation	Common designation	Sequence generated	Cp type	ret/ret (%)	ret/max (%)	max/max (%)	ret (%)	max (%)
Haploid Clementine	HCR	C. × clementina	7× Sanger	M	NA	NA	NA	89	11
Clementine mandarin	CLM	C. × clementina	110× Illumina	M	58	42	0	79	21
Ponkan mandarin	PKM	C. reticulata^a	55× Illumina	M	85	14	0.7	92	8
Willowleaf mandarin	WLM	C. × deliciosa	110× Illumina	M	91	8.8	0	95	4.4
W. Murcott mandarin	WMM	C. reticulata	25× Illumina	M	69	30	0.4	85	15
Chandler pummelo	CHP	C. maxima	22× Illumina	P	0	0.4	99.6	0.2	99.8
Low-acid pummelo	LAP	C. maxima	17× Illumina	P	0	0	100	0	100
Sweet orange	SWO	C. × sinensis	80× Illumina	P	14	82	3	55	44
Seville sour orange	SSO	C. × aurantium	36× Illumina	P	0	98	0	49	49

Three-letter abbreviations as used throughout this work and common systematic designation are shown. Sequence depth is reported as count of aligned reads to reference, after removal of duplicate reads. Chloroplast genome (Cp) type is inferred from shotgun reads aligning to the sweet-orange chloroplast genome³⁷, with M indicating mandarin type and P indicating pummelo type. Proportions of diploid nuclear genotype refer to the fraction of genome in megabases, according to the HCR physical map. (Proportions of unknown genotype are not shown but can be inferred by subtracting the three genotype proportions from 100%.) The last two columns show proportions of C. maxima (max) and C. reticulata (ret) haplotypes and are derived from the three genotype proportions. NA, not applicable.
^aPonkan mandarin is widely assumed to represent C. reticulata, but as shown here it has substantial admixture from C. maxima.

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